A citation-based method for searching scientific literature

Lawrence A David, Corinne F Maurice, Rachel N Carmody, David B Gootenberg, Julie E Button, Benjamin E Wolfe, Alisha V Ling, A Sloan Devlin, Yug Varma, Michael A Fischbach, Sudha B Biddinger, Rachel J Dutton, Peter J Turnbaugh. Nature 2014
Times Cited: 3912

List of co-cited articles
638 articles co-cited >1

Times Cited
  Times     Co-cited

Linking long-term dietary patterns with gut microbial enterotypes.
Gary D Wu, Jun Chen, Christian Hoffmann, Kyle Bittinger, Ying-Yu Chen, Sue A Keilbaugh, Meenakshi Bewtra, Dan Knights, William A Walters, Rob Knight,[...]. Science 2011

Human gut microbiome viewed across age and geography.
Tanya Yatsunenko, Federico E Rey, Mark J Manary, Indi Trehan, Maria Gloria Dominguez-Bello, Monica Contreras, Magda Magris, Glida Hidalgo, Robert N Baldassano, Andrey P Anokhin,[...]. Nature 2012

Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa.
Carlotta De Filippo, Duccio Cavalieri, Monica Di Paola, Matteo Ramazzotti, Jean Baptiste Poullet, Sebastien Massart, Silvia Collini, Giuseppe Pieraccini, Paolo Lionetti. Proc Natl Acad Sci U S A 2010

DADA2: High-resolution sample inference from Illumina amplicon data.
Benjamin J Callahan, Paul J McMurdie, Michael J Rosen, Andrew W Han, Amy Jo A Johnson, Susan P Holmes. Nat Methods 2016

Metagenomic biomarker discovery and explanation.
Nicola Segata, Jacques Izard, Levi Waldron, Dirk Gevers, Larisa Miropolsky, Wendy S Garrett, Curtis Huttenhower. Genome Biol 2011

Influence of diet on the gut microbiome and implications for human health.
Rasnik K Singh, Hsin-Wen Chang, Di Yan, Kristina M Lee, Derya Ucmak, Kirsten Wong, Michael Abrouk, Benjamin Farahnik, Mio Nakamura, Tian Hao Zhu,[...]. J Transl Med 2017

The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism.
Gijs den Besten, Karen van Eunen, Albert K Groen, Koen Venema, Dirk-Jan Reijngoud, Barbara M Bakker. J Lipid Res 2013

Environment dominates over host genetics in shaping human gut microbiota.
Daphna Rothschild, Omer Weissbrod, Elad Barkan, Alexander Kurilshikov, Tal Korem, David Zeevi, Paul I Costea, Anastasia Godneva, Iris N Kalka, Noam Bar,[...]. Nature 2018

Richness of human gut microbiome correlates with metabolic markers.
Emmanuelle Le Chatelier, Trine Nielsen, Junjie Qin, Edi Prifti, Falk Hildebrand, Gwen Falony, Mathieu Almeida, Manimozhiyan Arumugam, Jean-Michel Batto, Sean Kennedy,[...]. Nature 2013

A human gut microbial gene catalogue established by metagenomic sequencing.
Junjie Qin, Ruiqiang Li, Jeroen Raes, Manimozhiyan Arumugam, Kristoffer Solvsten Burgdorf, Chaysavanh Manichanh, Trine Nielsen, Nicolas Pons, Florence Levenez, Takuji Yamada,[...]. Nature 2010

From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites.
Ara Koh, Filipe De Vadder, Petia Kovatcheva-Datchary, Fredrik Bäckhed. Cell 2016

Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans.
Abigail J Johnson, Pajau Vangay, Gabriel A Al-Ghalith, Benjamin M Hillmann, Tonya L Ward, Robin R Shields-Cutler, Austin D Kim, Anna Konstantinovna Shmagel, Arzang N Syed, Jens Walter,[...]. Cell Host Microbe 2019

A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility.
Mahesh S Desai, Anna M Seekatz, Nicole M Koropatkin, Nobuhiko Kamada, Christina A Hickey, Mathis Wolter, Nicholas A Pudlo, Sho Kitamoto, Nicolas Terrapon, Arnaud Muller,[...]. Cell 2016

Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study.
Toshitaka Odamaki, Kumiko Kato, Hirosuke Sugahara, Nanami Hashikura, Sachiko Takahashi, Jin-Zhong Xiao, Fumiaki Abe, Ro Osawa. BMC Microbiol 2016

QIIME allows analysis of high-throughput community sequencing data.
J Gregory Caporaso, Justin Kuczynski, Jesse Stombaugh, Kyle Bittinger, Frederic D Bushman, Elizabeth K Costello, Noah Fierer, Antonio Gonzalez Peña, Julia K Goodrich, Jeffrey I Gordon,[...]. Nat Methods 2010

A core gut microbiome in obese and lean twins.
Peter J Turnbaugh, Micah Hamady, Tanya Yatsunenko, Brandi L Cantarel, Alexis Duncan, Ruth E Ley, Mitchell L Sogin, William J Jones, Bruce A Roe, Jason P Affourtit,[...]. Nature 2009

Gut microbiota composition correlates with diet and health in the elderly.
Marcus J Claesson, Ian B Jeffery, Susana Conde, Susan E Power, Eibhlís M O'Connor, Siobhán Cusack, Hugh M B Harris, Mairead Coakley, Bhuvaneswari Lakshminarayanan, Orla O'Sullivan,[...]. Nature 2012

Microbiome Datasets Are Compositional: And This Is Not Optional.
Gregory B Gloor, Jean M Macklaim, Vera Pawlowsky-Glahn, Juan J Egozcue. Front Microbiol 2017

Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.
Qiong Wang, George M Garrity, James M Tiedje, James R Cole. Appl Environ Microbiol 2007

Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors.
Bertrand Routy, Emmanuelle Le Chatelier, Lisa Derosa, Connie P M Duong, Maryam Tidjani Alou, Romain Daillère, Aurélie Fluckiger, Meriem Messaoudene, Conrad Rauber, Maria P Roberti,[...]. Science 2018

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.
Christian Quast, Elmar Pruesse, Pelin Yilmaz, Jan Gerken, Timmy Schweer, Pablo Yarza, Jörg Peplies, Frank Oliver Glöckner. Nucleic Acids Res 2013

Enterotypes of the human gut microbiome.
Manimozhiyan Arumugam, Jeroen Raes, Eric Pelletier, Denis Le Paslier, Takuji Yamada, Daniel R Mende, Gabriel R Fernandes, Julien Tap, Thomas Bruls, Jean-Michel Batto,[...]. Nature 2011

High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome.
Francesca De Filippis, Nicoletta Pellegrini, Lucia Vannini, Ian B Jeffery, Antonietta La Storia, Luca Laghi, Diana I Serrazanetti, Raffaella Di Cagno, Ilario Ferrocino, Camilla Lazzi,[...]. Gut 2016

American Gut: an Open Platform for Citizen Science Microbiome Research.
Daniel McDonald, Embriette Hyde, Justine W Debelius, James T Morton, Antonio Gonzalez, Gail Ackermann, Alexander A Aksenov, Bahar Behsaz, Caitriona Brennan, Yingfeng Chen,[...]. mSystems 2018

Dynamics of Human Gut Microbiota and Short-Chain Fatty Acids in Response to Dietary Interventions with Three Fermentable Fibers.
Nielson T Baxter, Alexander W Schmidt, Arvind Venkataraman, Kwi S Kim, Clive Waldron, Thomas M Schmidt. mBio 2019

Diet-microbiota interactions and personalized nutrition.
Aleksandra A Kolodziejczyk, Danping Zheng, Eran Elinav. Nat Rev Microbiol 2019

Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns.
Maria G Dominguez-Bello, Elizabeth K Costello, Monica Contreras, Magda Magris, Glida Hidalgo, Noah Fierer, Rob Knight. Proc Natl Acad Sci U S A 2010

Population-level analysis of gut microbiome variation.
Gwen Falony, Marie Joossens, Sara Vieira-Silva, Jun Wang, Youssef Darzi, Karoline Faust, Alexander Kurilshikov, Marc Jan Bonder, Mireia Valles-Colomer, Doris Vandeputte,[...]. Science 2016

Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities.
Patrick D Schloss, Sarah L Westcott, Thomas Ryabin, Justine R Hall, Martin Hartmann, Emily B Hollister, Ryan A Lesniewski, Brian B Oakley, Donovan H Parks, Courtney J Robinson,[...]. Appl Environ Microbiol 2009

The treatment-naive microbiome in new-onset Crohn's disease.
Dirk Gevers, Subra Kugathasan, Lee A Denson, Yoshiki Vázquez-Baeza, Will Van Treuren, Boyu Ren, Emma Schwager, Dan Knights, Se Jin Song, Moran Yassour,[...]. Cell Host Microbe 2014

Diet-induced extinctions in the gut microbiota compound over generations.
Erica D Sonnenburg, Samuel A Smits, Mikhail Tikhonov, Steven K Higginbottom, Ned S Wingreen, Justin L Sonnenburg. Nature 2016

Diets that differ in their FODMAP content alter the colonic luminal microenvironment.
Emma P Halmos, Claus T Christophersen, Anthony R Bird, Susan J Shepherd, Peter R Gibson, Jane G Muir. Gut 2015

The impact of diet and lifestyle on gut microbiota and human health.
Michael A Conlon, Anthony R Bird. Nutrients 2014

Dominant and diet-responsive groups of bacteria within the human colonic microbiota.
Alan W Walker, Jennifer Ince, Sylvia H Duncan, Lucy M Webster, Grietje Holtrop, Xiaolei Ze, David Brown, Mark D Stares, Paul Scott, Aurore Bergerat,[...]. ISME J 2011

A randomised trial of the effect of omega-3 polyunsaturated fatty acid supplements on the human intestinal microbiota.
Henry Watson, Suparna Mitra, Fiona C Croden, Morag Taylor, Henry M Wood, Sarah L Perry, Jade A Spencer, Phil Quirke, Giles J Toogood, Clare L Lawton,[...]. Gut 2018

Personalized Nutrition by Prediction of Glycemic Responses.
David Zeevi, Tal Korem, Niv Zmora, David Israeli, Daphna Rothschild, Adina Weinberger, Orly Ben-Yacov, Dar Lador, Tali Avnit-Sagi, Maya Lotan-Pompan,[...]. Cell 2015

Short Chain Fatty Acids (SCFAs)-Mediated Gut Epithelial and Immune Regulation and Its Relevance for Inflammatory Bowel Diseases.
Daniela Parada Venegas, Marjorie K De la Fuente, Glauben Landskron, María Julieta González, Rodrigo Quera, Gerard Dijkstra, Hermie J M Harmsen, Klaas Nico Faber, Marcela A Hermoso. Front Immunol 2019

Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota.
Marie Vétizou, Jonathan M Pitt, Romain Daillère, Patricia Lepage, Nadine Waldschmitt, Caroline Flament, Sylvie Rusakiewicz, Bertrand Routy, Maria P Roberti, Connie P M Duong,[...]. Science 2015

Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy.
Ayelet Sivan, Leticia Corrales, Nathaniel Hubert, Jason B Williams, Keston Aquino-Michaels, Zachary M Earley, Franco W Benyamin, Yuk Man Lei, Bana Jabri, Maria-Luisa Alegre,[...]. Science 2015

Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients.
V Gopalakrishnan, C N Spencer, L Nezi, A Reuben, M C Andrews, T V Karpinets, P A Prieto, D Vicente, K Hoffman, S C Wei,[...]. Science 2018

Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells.
Yukihiro Furusawa, Yuuki Obata, Shinji Fukuda, Takaho A Endo, Gaku Nakato, Daisuke Takahashi, Yumiko Nakanishi, Chikako Uetake, Keiko Kato, Tamotsu Kato,[...]. Nature 2013

A metagenome-wide association study of gut microbiota in type 2 diabetes.
Junjie Qin, Yingrui Li, Zhiming Cai, Shenghui Li, Jianfeng Zhu, Fan Zhang, Suisha Liang, Wenwei Zhang, Yuanlin Guan, Dongqian Shen,[...]. Nature 2012

An obesity-associated gut microbiome with increased capacity for energy harvest.
Peter J Turnbaugh, Ruth E Ley, Michael A Mahowald, Vincent Magrini, Elaine R Mardis, Jeffrey I Gordon. Nature 2006

Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans.
Brian D Muegge, Justin Kuczynski, Dan Knights, Jose C Clemente, Antonio González, Luigi Fontana, Bernard Henrissat, Rob Knight, Jeffrey I Gordon. Science 2011

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian C Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar,[...]. Nat Biotechnol 2019

Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.